def test_5ala_2_hop(self):
        filename = "temp.inp"
        otherfile = self.fixtures + "/5ala_2_hop.fixture"
        molecule = fileToMol("tests/5ala.xyz")
        fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
        fragmentation.setQMBasis('3-21G:6-31G*')
        fragmentation.setFMOHOPFragmentation()
        fragmentation.beginFragmentation()
        fragmentation.doFragmentation()
        fragmentation.finishFragmentation()
        directories = {'share': 'share'}
        gamessfmo = GamessFMO(fragmentation, directories)
        gamessfmo.setCentralFragmentID(1)
        gamessfmo.setBoundariesFromString("1.0")
        gamessfmo.setup()
        gamessfmo.writeFile(filename)
        generated = ReadStringListFromFile(filename)
        fixture = ReadStringListFromFile(otherfile)

        self.assertEqual(len(generated), len(fixture))
        for i in range(len(fixture)):
            self.assertEqual(generated[i], fixture[i])

        self.delete_file(filename)
    def test_water_5(self):
        filename = "temp.inp"
        otherfile = self.fixtures + "/water_5.fixture"
        molecule = fileToMol("tests/watercluster4.xyz")
        fragmentation = Fragmentation(molecule, defaults=FragItDataFMO)
        fragmentation.beginFragmentation()
        fragmentation.doFragmentation()
        fragmentation.finishFragmentation()
        directories = {'share': ''}
        gamessfmo = GamessFMO(fragmentation, directories)
        gamessfmo.setCentralFragmentID(1)
        gamessfmo.setBoundariesFromString("1.0")
        gamessfmo.setActiveAtomsDistance(1.0)
        gamessfmo.setBufferMaxDistance(1.0)
        gamessfmo.setup()
        gamessfmo.writeFile(filename)
        generated = ReadStringListFromFile(filename)
        fixture = ReadStringListFromFile(otherfile)

        self.assertEqual(len(generated), len(fixture))
        for i in range(len(fixture)):
            self.assertEqual(generated[i], fixture[i])

        self.delete_file(filename)